If Charlie were ever integrated back into society, and Starfleet decided he had killed those people, Charlie would have to serve time in a prison, which couldn't end well.

Not in the TOS context, he wouldn't. He would be sent to get therapy in an asylum, and if that didn't work, he'd be sent to Elba II until he got cured (which might be life, but apparently would only be until "Whom Gods Destroy" when an universal cure for the final incurables appears to be introduced). No set length of incarceration, no punitive angle to it.

I mean, look what happened to Lenore Karidian. She murdered half a dozen people, and got the therapy. Probably folks like "Lethe" were mass murderers or worse, too, before receiving their therapy; it's just that Dr. Adams practiced a variant of it that wasn't exactly accepted, and got poor Lethe as the result. Other asylums would produce better reformed murderers.

As an aside, oxygen deprivation probably isn't that big a problem in the TOS era: lungs can be entirely bypassed and tri-ox injected into the blood instead. And it's something found in every paramedic's pouch, apparently. So rescue before extensive brain damage is certainly a possibility, although far from a given.